During recent discussions on phylogeny, we saw a distinct failure to communicate, probably felt by both sides. The ‘evos’ attempted to consider the role of molecular data in determining relationship. Given that an obvious cause of common sequence is common descent, due to the significant but not perfect fidelity of the DNA replication process, the phylogenetic inference is that sequence similarity is indicative of common descent. This, critics feel, is a circular argument.
In this, they may be following Jonathan Wells in Icons of Evolution. His criticism is that “homology is inferred from common ancestry, then turned around and used as evidence for common ancestry”. Yet in molecular genetics, the term ‘homology’ tends to be used to indicate sequence similarity alone, not a descent relationship. DNA probes and separate-strand annealing rely upon ‘high homology’, meaning only complementary sequence. The similarity is an observation, not an inference. If one had two sequences, XXXXXXXY and XXXXXXXZ, they certainly aren’t inferred to be similar: they really are similar. The retention of similarity (with variations) in a line of descent is also an observation. It is not clear to me where the circularity comes in in putting those two observations together and inferring that sequence similarity is supportive of common descent. Particularly when other sites are brought in to the analysis. Each site verifies the assumption for the other(s); Creationists on the other hand lump the whole into a composite sequence, and expect ‘independence’ to come from something other than sequence identity. You can’t verify genes using genes, or something.
Well, if the argument is circular, we must apply that razor to within-species comparisons as well – paternity testing, forensics, molecular genealogy and ethnic investigations must all be based upon circular reasoning too. Which I suspect no-one would try and argue in court. Broadening this out to between-gene-pool sequence similarity, among species that are even termed ‘closely related’, we presumably don’t have a major problem with sequence being commonly derived from a common ancestor there either. So the question is: as one goes ‘upwards’ in the Linnaean classification system, where does the circularity arise, if it is not there throughout? The differences identified between higher taxa are inevitably greater than those at lower, as one would expect from the same process of descent with modification that explains similarity among relatives, extended in time. As time goes on, the similarities erode and the differences increase. But there is no boundary detectable, no clear transition at which ‘circular reasoning’ comes in, nor where there is an abrupt difference as would be expected from separate origins. Differences remain a matter of degree, albeit confounded by rare events and inevitable statistical artefacts.
The Creationist alternative for sequence similarity is ‘Common Design’. I confess I can never make any sense of this. At what point does Common Descent stop and Common Design take over? In a process whereby a Designer generated in initial version of a sequence, and then allowed nature to take its course, the similarities between subsequent lineages would actually be due to Common Descent, not the initial Design.
OK, we might propose a Designer making separate taxa. The similarities in sequences between any two such taxa could be termed Common Design. But members of Taxon A and Taxon B are still commonly descended from that point on, from the moment of creation. So you can never separate out Common Design completely from Common Descent. In any process where similarities were initiated by Common Design, residual within-taxon similarities still indicate Common Descent from those points. The exact same kind of data has two completely different explanations across that assumed boundary, which is extravagant and inconsistent. The boundary is not a real boundary in the data.
If we follow the differences in Taxons A and B back, attempting to reverse out evolutionary history, we get to a point where the ‘ur-sequences’ exhibit a high degree of sequence similarity. Something which, if we observed it today, would strongly support a genetic relationship. So what would persuade us that, at that point in history, the relationship was not, in fact, genetic?
Common Design is sometimes invoked as ‘like creatures need like DNA’. But if we envisage the Design occurring at a high enough taxonomic level, we are saying that some very unalike ‘creatures’ had like DNA, at the moment they were … created. They only have unalike DNA now, after a few million years of separate change.
Further, none of this helps explain genetic similarities at loci that have little to do with phenotypic difference. One of the principal markers used in paternity testing are SINEs – a kind of transposon. Intergenic examples have no apparent phenotypic effect, and vary in humans (obviously, or they’d be no use). But there are also SINE inserts that are held in common between humans and chimps, others that are diagnostic at still higher taxonomic levels. They can’t all be essential to the form of the members of the clade they are restricted to – can they?
I’ve taken a somewhat circuitous route to my point, and the reason for the title. Consider the following not-very-treelike tree.
It represents the result of extensive phylogenetic analysis of the entire eukaryote clade. Reminiscent of those ‘you are here’ pictures of the Milky Way, ‘animals’ are all stuffed in the red box at bottom right. That’s everything: vertebrates, insects, sponges, nematodes … Fungi are just above, and land plants, seaweeds and Volvocales at about 11 o’clock. That’s pretty much it for multicellular life. The tree overwhelmingly consists of unicellular eukaryotes of bewildering diversity – what used to be called protists, and still are when we aren’t being cladistically rigorous. Never mind beetles, thats what the designer has an inordinate fondness for! If we had no place on this tree, I suspect people would have no problem with it, or the methods used to infer it. Of course we notice the multicellular life more than anything else. They’re bigger. It’s us, it’s our pets, food, materials and enemies. But most of the tree is minute, and does not indulge colonial clumping, amendments of which cause the ‘mechanical impossibility’ arguments ranged against phylogeny.
The discussions involved in resolving and testing these ‘protistan’ branches are surprisingly heated. It’s not just a question of assuming a relationship; the relationships are teased out of the data. If there were no relationship, that too would be apparent from the data. So where, in the progression to the interior of this diagram, and trying not to be bamboozled by the contents of that little red box, does circular reasoning come into it? Likewise, where does Common Design take over from Common Descent as the cause of similarity?
Baloney, the diagram I drew myself above and which I posted here almost two weeks ago in another thread uses the term Cyclostome fish. Right there when I have it staring in your face you’ll make a untrue claim.
Like I said, you just reflexively say I don’t understand. Just like you denigrated the use of Smith-Waterman or alignment algorithms, and now you have to admit Phylogenetic analysis won’t even get off the ground without it.
I was pointing out Smith-Waterman is a relatively unbiased unambiguous comparison, and you poo-pooed the fact birds didn’t look like cyclostomes or teolosts, but they looked like birds! I added that I don’t currently have the data for lungfish and coelecanths. Given your reluctance to suggest accession numbers despite you claiming to be an expert, I’ll go look myself.
John Harshman,
Exactly, if you observe apples falling out of trees repeatably you can then infer that when an apple stem is separated from a tree limb it will fall to the ground.
If we can observe two species diverging from a common ancestor then we can infer that this happens with other species? If we never observed it happening one time, how can we infer it is a repeatable occurrence?
Gravitational effect is a process you can model.
Two specie’s splitting from a common ancestor is also a process that requires isolated populations and random variation. How would you model it? What observation would you use to model it?
If you can figure out how it happened your chances are much better of creating an accurate inference across a diverse set of species.
Love the wake in the picture. That’s about as close as a still shot will ever come to explaining the locomotion.
Right. He readily accepts that birds are dinosaurs, because some non-avian dinosaurs had feathers.
There are evolutionary models. It’s almost trivial to model evolution. The accurate analogy would be, how did gravity produce what we currently see in the Solar System for example? What observation would you use to model how the rings of Saturn formed? Were you there? Were you? Eh? Were you there or what?
colewd,
Until the last interfertile individuals die, the species can hybridise and you would insist they are not separate species. When they have died, the species cannot hybridise and you would insist that we have no means of determining their common ancestry. Neat! We would actually have to watch them die, and know that they were the last interfertile individuals, to satisfy your bizarre criterion.
Meantime, the genomes of both interfertile and non-interfertile populations are stuffed to the goddamned gunwhales with commonality, and not just in functional sequence. It is that very commonality that permits the hybridisation which is the latest attempt to apply a ‘permissible’ criterion of common descent. Yet when we analyse it ourselves, rather than letting syngamy and meiosis examine it (‘experimentally’), we need to demonstrate the entire speciation process, exhaustively, before we can infer common descent? This is very inconsistent.
The reality is, the kind of transitions occurring at the species boundary are pretty trivial. They aren’t complete rewirings of the heart, or fish taking off from the sea and forgetting to land. It is rather ridiculous to assume it infeasible without experimental demonstration – it is an inevitable consequence of genetic divergence: progressive reduction in prezygotic and postzygotic compatibility. You can tell that is happening through … molecular analysis! That thing that is inadmissible in the evolutionary court, except when it isn’t.
It’s not what happens then that leads to the kind of ‘infeasible’ transitions touted, it is what happens later, through ongoing divergence between the lineages. It’s not really a transition as imagined. People are imagining it all happening at once, and challenging evolutionists to explain how it all happens at once. The reply is “it doesn’t …”.
If we can observe a craton forming out of the boundless ocean, then we can infer that this happens with other cratons. If we never observed it happening one time, how can we infer it is a repeatable occurrence?
Maybe evidence isn’t all about real-time observation.
Glen Davidson
I’m not sure you know what “cyclostome fish” are. At any rate your diagram is what’s called a star phylogeny. It isn’t a branching diagram. A proper tree would look like the one I hope is at the end of this post. Note several differences from yours. First, it’s based on real data. Second, it shows actual branching, with some taxa more closely related to each other than others. (I’m afraid there are no cyclostomes, but there is a lungfish, which makes the point that birds are more closely related to some fish than others.)
I will repeat: You don’t understand. That isn’t reflex. I’m just looking at what you say, which contains much nonsense. I have never denigrated the use of alignment algorithms, though there are better ones than the one used by BLAST.
Again, please don’t insult me. It isn’t that I claim to be an expert. I actually am. You may not agree with me, but you should at least acknowledge that I do know something about the subject, while you don’t.
I swear I did the “upload file” thing with a pdf, yet nothing appears except the title “vests.pdf”. Even clicking on that gives me nothing. Is there something wrong with the way this site treats pdfs?
Allan Miller,
In most science we have direct observation or experiment to create a scientific inference. When using all 5 steps of the scientific method you have both. In the case of the common ancestor hypothesis you have neither. You have historical data which you can create an inference but this data only directly tells you there is a relationship. The common ancestor hypothesis identifies a very specific relationship, which is a logical leap based on the available data.
No, we don’t. Consider particle physics: have you ever seen an electron, a proton, a neutrino, or even an atom? Nope. Yet we know they exist. Why? Inference from what we can observe. Similarly, though we have rarely (though not quite never) seen a species split into two species, we know it happens and has happened on particular occasions in the past, based on observable data. As with most creationists, you have a different standard for science that doesn’t contradict your beliefs than for science that does.
Yeah, and I can reasonably predict after 300 million years, or some N-generations, descendants of a coelacanth fish will be a coelacanth fish, descendants a lungfish a lungfish. Neither line will create a bird. Absolutely no expectation from what we directly observe it will be different for any other fish! NONE! Oh and by the way, surprise surprise the coalecanth was thought to be extinct and until we found them! And guess what, we could still relate the modern one to the ancient one because they looked so similar and it confirms that fish are expected to have fish-like descendants. That is scientific expectation, something evolutionary biology seems to be willing to state. Expected results, expected outcomes, expected values…lots of sciences have these.
Here is the “phylogeny” of tetrapods in relation to other fish and creatures like lungfish and coelecanths:
https://en.wikipedia.org/wiki/Sarcopterygii#Phylogeny
Any evolutionist willing to volunteer what creature in the fossil record is the ancestor of lungfish, coelecanths and tetrapods in that diagram — the ancestor Sarcopterygii? Out with it guys, name the fossil or say the ancestor doesn’t exist in the fossil record.
You say I don’t understand, OK name the fossil, where it was found, provide a photo of the fossil if possible.
So if you don’t have a fossil ancestor, don’t have a morphological description, don’t have a molecular description, you’ll insist in the absence of direct evidence some fish-like creature had a descendant that was a bird.
colewd,
Ever observe a mountain being formed?
Heavens, lectures in the scientific method from a creationist …
So how can you apply the ‘common ancestor hypothesis’ at one taxonomic level but not at another? You seem determined to miss this point. You should reject ALL ancestry inference based upon sequence relation if you did not observe the events assumed, if that’s the way you’re going to go about things. Including forensics and paternity.
stcordova,
It is a rather inescapable conclusion based upon the data.
I can certainly agree that there is little danger of your claim being falsified. A brave prediction indeed.
If I may paraphrase, you’re saying “If we come from monkeys, why are there still monkeys?” Right?
How do you expect me to stop saying you don’t understand when you show it time after time like that? I swear I’ve posted this sort of thing many times before:
1. Given the fragmentary nature of the fossil record, we are unlikely to find the direct ancestor of any clade preserved.
2. Even if we find it, we can’t recognize it, as we have no way to distinguish that ancestor from a species that is cousin to that ancestor.
3. But cousins are good enough for many purposes, including the one here. Let me suggest that Eusthenopteron, Panderichthys, and Tiktaalik are all good stand-ins for fish that are ancestral to tetrapods. The common ancestor of lungfish, coelacanths, and tetrapods would be something else, and off the top of my head I can’t think of the name of a close cousin of that ancestor, but any paleontology text should give you a good idea.
4. While we don’t and can’t identify any actual fossils as ancestors, we certainly do have morphological and molecular descriptions of them. That’s how we can recognize cousins.
5. I could provide a long line of fossil cousins that, lined up, would show a gradual transformation from something you would call a fish to something you would call a bird. If nothing else, that shows it to be “mechanically feasible”.
6. You are asking for evidence beyond that needed and far beyond that you consider necessary for many things you accept as true. You think you’re descended from Adam? Show me his body. You think great oaks from little acorns grow? Show me a movie of such a thing happening. You think carbon atoms have 6, 7, or 8 neutrons? Where’s the photo? For that matter, show me a neutron.
Natural Selection in a nutshell.
And when the morphological description doesn’t fit, you use the molecular one. And when the molecular one doesn’t fit, you chose the morphological one.
And if neither fits, you say the fossil record is incomplete.
That is why you can’t lose.
First things first.
It is just a line of reasoning. Thats the important point.
So if there are other options for the MERE reasoning then it nullify’s the REASONING of evolutionism as the only option.
So with other options it ends EVIDENCE of common descent from genetic trails.
Like looks would have like dna from a like blueprint. No reason to see common descent as the origin for like dna.
Evolutionism has been logically careless about this and so its conclusions using dna are not scientific in being of a inclusive investigation.
It was just a first quick hunch.
Still is. I always have to spell out its just a line of reasoning and not scientific genetic evidence.
True or not.
its all comparitiveness in these matters.
Laugh all you want, but I don’t see this as being very different than what Sal and colewd are saying.
I don’t see this as being very different from what Sal and colewd are saying.
You’ve got to admit, though, that they manage to get even more facts wrong than Robert.
That’s what greater knowledge is about for the creationist, more ways of screwing up the data.
Glen Davidson
I looked at some literature, suggested proteins and genes for PHYLIP Dayhoff PAM matrix study:
α and β haemoglobin proteins,
18S rRNA and 28S rRNA,
cytochrome oxidase subunit 1,
major histocompatibility complex (MHC) class 1,
12S rRNA and 16S rRNA,
the enolase protein family
cytochrome b
Hox cluster genes
This will take some time to gather the data and process it….
So, here are the clades leading to humans, so in the DIRECT line to humans as far as actual fossils go:
Sarcoptergyii ancestor : missing
Rhipisdistia ancestor : missing
Tetrapodomorpah ancestor: missing
Eotetrapodiformes ancestor: missing
Elpistostegalia ancestor: missing
Stegocephalia ancestor: missing
Synapsida ancestor: missing
Eupelycosauria ancestor: missing
Sphenachodontia ancestor: missing
Thereapsida ancestor: missing
Eutherapsida ancestor: missing
Neotherapsida ancestor: missing
Theriodonitia ancestor: missing
Eutheriodontia ancestor: missing
Cynodontia ancestor: missing
Probainognathia ancestor: missing
Mammalia ancestor: missing
Theria ancestor: missing
Placentalia ancestor: missing
Boreoeutheria ancestor: missing
Euarchontoglires ancestor: missing
Euachonta ancestor: missing
Primatomropha ancestor: missing
Primate ancestor : missing
Chimp Human ancestor: missing
But you believe the creatures in the line to humans existed. Why? Despite lack of fossils and despite lack of direct experiment. Direct experiment shows birds descend from birds, and fish from fish. That is the natural expectation. Evolution theory on the other hand only pretends to be a naturalistic theory, but when pressed for details, it invokes events indistinguishable from miracles. Why do you think hopeful monster theory was popular for a season?
Sal,
The objective nested hierarchy shows that common descent fits the evidence trillions of times better than common design, and that unguided evolution fits the evidence trillions of times better than ID — even ID in the form of guided evolution.
See
Things That IDers Don’t Understand, Part 1 — Intelligent Design is not compatible with the evidence for common descent
The battle was over long before you put on your toy armor, Sal.
The evolutionary story goes like this: There is a missing link ancestor of the the Lobe-Finned fishes (Sarcopterygii) — let’s call it the Mother-of-all-lobed-finned-fishes.
The mother-of-all-lobed-fined fishes had 3 cousin/sister lines of descendants that exist to this day.
1. Actinistia Coelecanths which stayed coelecanths for more than 300 million years
2. Rhipidistia Lungfish which stayed lungfish for more than 300 million years
3. Rhipidistia Tetramorpha which uh…..over 300 million years became birds, tigers, giraffes, turtles, sharks, whales, dolphins, cows, frogs
So in two existing lines (coelecanths and lungfish), the creatures stayed the same for 300 or more million years, not very much change, whereas the 3rd line (Tetramorpha) evolved into all the tetrapods.
Scientific theories should bear the mark of expected outcomes form initial conditions. If the initial condition is a lobed-finned fish, then after 300 million years what should be the expected outcome? Should it be a lobed-finned fish or a bird? Two direct reasonable observations say it should be a lobed-finned fish (coelecanths and lungfish) where as one speculative observation with no experimental evidence says it will be tetrapods of birds, giraffes, frogs, cows, whales, bats, etc.
If a theory can’t state expectations from initial conditions, then its status as a scientific theory is questionable.
For all we know, the supposed rapid diversification of tetramorpha is a product of imagination since the sister/cousin groups of lungfish and coelecanths remained so persistent, and the other line of tetramorpha diversified like crazy. Added to this, there are missing links in every step. That suggests to me taxonomic nested hierarchy wasn’t generated by a lobe-finned-fish ancestor diversifying into the tetrapods.
Or you have fundamentally misunderstood something along the way?
Can you put your objective hat on for a moment and propose some reasons why that might have been the case?
I look forwards to reading your paper on your alternative proposal.
Well well well, John Harshman who so denigrates the BLAST incarnation of Smith-Waterman, will be unpleased to know it was used to establish the close “phylogenetic” relationship of lungfish and coelecanths.
Also:
43 genes support the lungfish-coelacanth grouping related to the closest living relative of tetrapods with the Bayesian method under the coalescence model
So much claiming the Tree of Life project has no competing alternative phylogenetic trees.
Which means, TADA, birds are not lobed-finned fishes, they are birds. Lobe-finned fishes are lobed-finned fishes. 🙂
Yet none of this offers any support for any position other then non-supernatural evolution. So what’s your point? Yes, no doubt some people are wrong about some things but nobody is wrong about non-supernatural evolution.
If your sole point is to take two positions and note that they are two positions and therefore supernatural, then good luck with that. You’ll be wasting your life, but whatevers.
John Harshman,
Indeed, and I have tried the same tack with them without success. A ‘line of reasoning’ admissible at one taxonomic level is inadmissible at another, with no reason given beyond the fact that it fails their intuition test. And something about ‘missing links’.
stcordova,
I swear, this is less about science than the service of you own ego. You have spent many a happy hour Googling over the years for the reference that you think makes your interlocutor look silly.
stcordova,
Who on earth has claimed this?
That is something of a non-sequitur. And are you really using phylogenetic analysis of the basal relationships to support your contention that birds are not commonly descended with the rest of the tetrapod clade?
Fucking Douglas Theobald, using phylogenetics to contribute to medical knowledge:
Using ancient protein kinases to unravel a modern cancer drug’s mechanism
C. Wilson1,*, R. V. Agafonov1,*, M. Hoemberger1, S. Kutter1, A. Zorba1, J. Halpin1, V. Buosi1, R. Otten1, D. Waterman1, D. L. Theobald2, D. Kern1,†
Key question for ID-creationists: If evolution didn’t actually happen, why can an ancestral state, different from it’s extant descendants, be inferred, physically reconstructed and tested to be functional in the laboratory? Shouldn’t this kind of work be impossible if evolution didn’t happen? You know, “mechanically infeasible”?
Rumraket,
You must be trying to pull another Keiths Rumraket. Claim a paper says something important, post an abstract of the paper, then if the thing you want to claim isn’t there, just say, well, its in the full paper, go read it, because I am too busy to say what it is I am claiming…
You deserve the same answer as keiths, go read the Encyclopedia Britannica, it will show why you are wrong. Trust me.
Rumraket,
Just replace “mutation” with “miracle” and “common ancestor” with “special creation” and publish that in bio-complexity. Creation science FTW!
It took me literally 1 minute to find the complete paper
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405104/
Goes to show how much of a fucking charlatan you are
dazz,
It doesn’t take much longer to find the Encyclopedia Britannica either. But that does not help you to find where in it it shows that you are wrong, now does it Dazz?
You’re such a laugh. Still can’t figure out a simple binomial or poisson distribution? Still can’t wrap your head around the concept of fixation? yet you still think you’re in a position to challenge decades of work in evolutionary biology? Tell me more about your special creation myths…
stcordova,
A better understanding of speciation (essentially, the basal node of any common descent relationship in sexual eukaryotes) and the comparative likelihood of fossilisation at or near such a node might help here. If understanding is sought, that is.
Heh, funny thing is, what I’m claiming is right there in the abstract. The paper merely elaborates on it. As usual phoodoo’s propensity for own-goals is amazing. I also like how he’s still not aware I have him on ignore and the only reason I read his response is you quoted him.
I do have to concede that I was working on the assumption that the words in the abstract were comprehensible to phoodoo et al. My mistake.
Let’s try to put the argument into smaller digestible bits for the requisite IDiots:
Here are the IDiot premises we are to take for granted for this argument to work:
1. IDiots say mutations are overwhelmingly much more likely to destroy information or genetic sequences, than to produce new or improved functions.
2. IDiots say beneficial mutations are so rare as to be an absurdity to think they can have an effect on evolution.
3. IDiots say functional proteins with different functions, are too far apart in functional sequence space, for evolution to be able to cross those distances in the available timeframes (the ~4 billion year history of life on Earth).
4. IDiots say phylogenetic inferences are circular reasoning, that they do not actually constitute evidence of the reality of the inferred relationships, because the similarities are equally or better explained by “common design” than by common descent.
5. IDiots say phylogenetic inferences can’t be tested with experiments, because the divergences happened in the past.
With me so far? Good, so now we look at the paper and what the authors did:
1. Take a large number of extant enzyme sequences from Malate and Lactate dehydrogenases(those are names of enzyme families in the dehydrogenase superfamily).
2. Use them to build phylogenetic trees.
3. From the inferred tree, infer the most likely ancestral nodes(aka ancestors) using a substitution model. Those would be ancestral enzymes, as in proteins with amino-acid sequences that no longer exist. Enzymes that, if evolution is true, used to exist millions of years ago, but later mutated into what we see today.
4. Physically construct those inferred amino-acid sequences that no longer exist, and only SHOULD have existed IF evolution is true.
5. Test them biochemically in the lab for function.
Now for the argument:
If IDiots are right, the inferred phylogenetic relationships are false(IDiot premise 4).
If IDiots are right there IS no prior evolutionary history to the enzymes we find in extant life, they were independently created as-is, by a designer just re-using previous designs(IDiot premise 4).
If IDiots are right, inserting mutations into the proteins of extant life should BREAK their function, it should NOT be likely that new functions are found(IDiot premises 1, 2 and 3).
So this naturally raises some question: How the fuck was the results of the paper possible if IDiots are right?
How come phylogenetically inferring quite mutated versions of extant proteins, yields different but still functional proteins, with diferent functions? Shouldn’t mutations almost always result in degraded functions? Isn’t phylogenetics just circular reasoning? Isn’t this actually a test of the inferred phylogenies? Are IDiots stupid or just deliberately ignorant?
We hypothesise that limbs evolved gradually from fins. But does the evidence justify this scenario. Imagine that we had before us a series of nine leaves We don’t know where they came from but they were in fact taken from the stem of a buttercup. We examine their form and see that they display a certain relationship. By this we can place them in a certain order of similarity. We might surmize that each one went through a stage where it was the same shape as the leaf preceeding it and that there are missing links between the samples that we have not been given. But we would be wrong. The shapes are distinct and are not explained by a historical linkage. Each leaf did not pass through a stage where it more closely resembled the one preceeding it.
Ronald Bradly discusses the connection between fins and limbs here
To see a drawing of the various stages of buttercup leaves see fig 2.2 in the essay linked to above.
This is all very cute, but individual leaves don’t leave mutated descendants before they die(they don’t reproduce imperfectly), whole organisms do. Your argument fails at a fundamental level.
If organisms didn’t reproduce themselves there’d be no reason to think in terms of genealogical relationships in the first place. But they do, you can’t just elect to ignore such a fundamental property of life when seeking to explain patterns of shared derived characteristics.
Why do we think you came from two people that look a lot like you? Because we actually see that human beings leave descendants that look like them. The more distantly related, the more different they become.
At what point do you think patterns of nesting shared similarities crosses from “clearly indicates descent” into “clearly indicates a barrier a designer must overcome”?
and comments
True. But the funny thing is, after all that practice, he’s still not very good at it.
The authors Sal quotes did NOT use BLAST to establish the phylogenetic relationship. His technique resembles that of the hilarious Dionisio at UD: google; then highlight phrases he thinks support his position.
In reality, Sal’s citation is a wonderful GSW to the foot: Biscotti et al used BLAST to identify orthologs for their transcripts. They used BLAST all over the place (they used BLASTn to identify mitochondrial transcripts, for instance). And they used reciprocal BLASTp to select the 226 genes they would use for the phylogenetic analysis. But when it came time to actually do the phylogenetic analysis on those 226 genes, did they use BLAST?
No. They did not.
As anyone who actually read the paper would know.
Actually, it isn’t known whether the ancestors are in fact missing.
Rather, the issue is that from a rather simple observation of extant life, many highly similar organisms exist contemporaneously with each other. Suppose all but one lineage were to go extinct, but only 0.001% of them fossilize tomorrow, what are the odds that among that pool of fossilized species, the ancestor of one living a million years from now would be among them? Probably quite low. Factor in the odds that a paleontologist digging in a sediment a million years from now happens to find that one particular member of the actual ancestral lineage, rather than just a cousin species that is highly similar. Would he be justified in inferring that it probably WAS the actual ancestor? Not really.
That means that, even if we have something that constitutes a good morphological candidate for an actual ancestor, we cannot actually infer that it IS a direct ancestor with any noteworthy certainty, so we elect instead to represent it as a distantly related cousin in the tree of lifer, rather than pretend it is a direct ancestor. Because that is the most likely to be true option.
I wonder how many of YOUR ancestors we can go out and dig up directly. Are we now to infer you have none?
Bazinga!
It appears to my naïve and non-expert eye that Creationists are missing a major point regarding consilience of the Fossil Record with Bioinformatics. Forgive me if I am merely restating the blatantly obvious. My target audience here would be the few hold-out Creationists who obtusely seem to be missing a very obvious but important point.
The eyes of my high school students understandably glaze when I embark in too much detail on such cladistics esoterica so I simply cut to the chase:
Not only is there a paleontological fossil record – but there is a Genomic Fossil record. Our genome is littered with “DNA fossils”, DNA at one time expressed but no longer. For a great description accessible to the layman – I cite Neil Shubin’s excellent book: Your Inner Fish.
http://www.pbs.org/show/your-inner-fish/
My favorite classroom example would be commonalities between Avian and Dinosaur collagen amino acid sequences easily google-whacked by any who are interested.
This is of course ties into fascinating experiments where the growth of reptile-like tooth buds can be induced in birds (neat tie-in to primordial germ layer interactions in embryogenesis) – but only because birds still possess fossil DNA whose activation still permits the growth of teeth their ancestors once used (as indicated by the fossil record).
Of course, Creationists retort that such lines of conjecture are specious. If any of that were true, Science should be able (by appropriate genetic engineering) to convert a chicken into a dinosaur. Next, scientists will be telling us that Dinosaurs even had feathers!
How silly indeed… Hold those thoughts:
https://www.washingtonpost.com/national/health-science/paleontologist-jack-horner-is-hard-at-work-trying-to-turn-a-chicken-into-a-dinosaur/2014/11/10/cb35e46e-4e59-11e4-babe-e91da079cb8a_story.html
In short – arguments regarding sequence homology are not rendered “circular” when a plethora of such sequences are clearly identified as now-inactive “Fossil” DNA which can be reactivated in predictable fashion to generate outcomes that correspond to expectations according to the paleontological fossil record.
Of course, there is also the issue of commonalities of pseudogenes shared across lineages. Consilience-Squared!
It is about this point in my discussion of evidence for evolution that even my most reluctant students throw in their “religious” towel and concede the cogency of evolution. So I do not belabor the point too much more. Again, I apologize for wasting the time of those more expert than myself; as I said before, my target audience were obtuse Creationists who should choke before uttering “Fossil DNA” & “Intelligent Design” in the same breath.
Of course, there always will intellectually dishonest few who will resist the scientific method:
Lewis Black on « Fossils are the handiwork of the Devil »
https://www.youtube.com/watch?v=JKA1UNAu-dc
TomMueller,
And the answer is … Common Design! Yes, I know it’s a crap answer.